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annotate documentation/readme.rst @ 7:fcadce4d9a06 draft

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author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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1 ===============
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2 Bismark Wrapper
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3 ===============
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5 Bismark_ uses Bowtie or Bowtie2 to map bisulfite converted sequence reads to a reference genome and determine cytosine methylation states.
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6
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7 Publication: http://www.ncbi.nlm.nih.gov/pubmed/21493656
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9 User Guide: http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide_v0.7.12.pdf
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11 .. _bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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13 Preparation
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14 ===========
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16 Create your reference index with *bismark_genome_preparation* in your normal Galaxy Bowtie2/Botwie index directory. It will create a Bisulfite_Genome folder directly in your Bowtie2/Bowtie index directory.
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17 If you follow that approach you do not need to specify or modify an extra .loc file.
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18 That wrapper will extract the path to the Bisulfite_Genome folder from ./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.
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20 =======
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21 History
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22 =======
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24 - v0.7: Initial public release
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25 - v0.7.8: update and add Tool Shed Integration
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26 - v0.7.11.1 change default output to BAM, from now on samtools are required
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27 - v0.7.11.2 added multi-threading to samtools (samtools > 0.1.19 is required)
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28 - v0.7.12 upgrade to bismark 0.7.12 and fix a major slowdown
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29 - v0.7.12.1 define a dependency to samtools 0.1.19
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32 ===============================
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33 Wrapper Licence (MIT/BSD style)
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34 ===============================
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36 Permission to use, copy, modify, and distribute this software and its
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37 documentation with or without modifications and for any purpose and
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38 without fee is hereby granted, provided that any copyright notices
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39 appear in all copies and that both those copyright notices and this
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40 permission notice appear in supporting documentation, and that the
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41 names of the contributors or copyright holders not be used in
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42 advertising or publicity pertaining to distribution of the software
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43 without specific prior permission.
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44
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45 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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46 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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47 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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48 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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49 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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50 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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51 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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52 OR PERFORMANCE OF THIS SOFTWARE.
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